/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2020 UniPro <ugene@unipro.ru>
 * http://ugene.net
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
 * MA 02110-1301, USA.
 */

#ifndef _U2_MYSQL_ASSEMBLY_MULTI_TABLE_DBI_H_
#define _U2_MYSQL_ASSEMBLY_MULTI_TABLE_DBI_H_

#include <QReadWriteLock>

#include <U2Core/U2SqlHelpers.h>

#include "MysqlAssemblyAdapter.h"
#include "util/AssemblyPackAlgorithm.h"

namespace U2 {

class MysqlDbi;
class MysqlSingleTableAssemblyAdapter;
class MysqlSingleTablePackAlgorithmAdapter;

class MysqlMtaSingleTableAdapter {
public:
    /** Wrapper over 1 table in database. If singleTableAdapter == NULL the table was not created yet */
    MysqlMtaSingleTableAdapter(MysqlSingleTableAssemblyAdapter *adapter, int rowPos, int elenPos, const QByteArray &extra);

    MysqlSingleTableAssemblyAdapter *singleTableAdapter;
    int rowPos;
    int elenPos;
    QByteArray idExtra;
};

class MysqlMultiTableAssemblyAdapter : public MysqlAssemblyAdapter {
public:
    MysqlMultiTableAssemblyAdapter(MysqlDbi *dbi, const U2DataId &assemblyId, const AssemblyCompressor *compressor, MysqlDbRef *ref, U2OpStatus &os);
    ~MysqlMultiTableAssemblyAdapter();

    virtual qint64 countReads(const U2Region &region, U2OpStatus &os);

    virtual qint64 getMaxPackedRow(const U2Region &region, U2OpStatus &os);
    virtual qint64 getMaxEndPos(U2OpStatus &os);

    virtual U2DbiIterator<U2AssemblyRead> *getReads(const U2Region &region, U2OpStatus &os, bool sortedHint = false);
    virtual U2DbiIterator<U2AssemblyRead> *getReadsByRow(const U2Region &region, qint64 minRow, qint64 maxRow, U2OpStatus &os);
    virtual U2DbiIterator<U2AssemblyRead> *getReadsByName(const QByteArray &name, U2OpStatus &os);

    virtual void addReads(U2DbiIterator<U2AssemblyRead> *it, U2AssemblyReadsImportInfo &ii, U2OpStatus &os);
    virtual void removeReads(const QList<U2DataId> &readIds, U2OpStatus &os);
    virtual void dropReadsTables(U2OpStatus &os);

    virtual void pack(U2AssemblyPackStat &stat, U2OpStatus &os);
    virtual void calculateCoverage(const U2Region &region, U2AssemblyCoverageStat &coverage, U2OpStatus &os);

    virtual void createReadsIndexes(U2OpStatus &os);

    int getElenRangePosByLength(qint64 readLength) const;
    int getElenRangePosById(const U2DataId &id) const;
    int getNumberOfElenRanges() const;

    int getRowRangePosByRow(quint64 row) const;
    int getRowRangePosById(const U2DataId &id) const;
    int getRowsPerRange() const;

    const QVector<MysqlMtaSingleTableAdapter *> &getAdapters() const;
    const QVector<QByteArray> &getIdExtrasPerRange() const;

    MysqlDbRef *getDbRef() const;

    MysqlMtaSingleTableAdapter *getAdapterByRowAndElenRange(int rowRange, int elenRange, bool createIfNotExits, U2OpStatus &os);

private:
    QString getTableSuffix(int rowRange, int elenRange);
    static QByteArray getIdExtra(int rowRange, int elenRange);

    /** Checks if table info must be re-read from DB and calls re-read if needed */
    void syncTables(U2OpStatus &os);

    /** For a new and empty assembly analyzes reads data and calculate ranges */
    void initTables(const QList<U2AssemblyRead> &reads, U2OpStatus &os);

    /** Re-reads table info from DB */
    void rereadTables(const QByteArray &idata, U2OpStatus &os);

    /** Flushes tables info into database */
    void flushTables(U2OpStatus &os);

    void clearTableAdaptersInfo();

    MysqlMtaSingleTableAdapter *createAdapter(int rowRange, int elenRange, U2OpStatus &os);

    void initAdaptersGrid(int nRows, int nRanges);

    MysqlDbi *dbi;

    /** All non-NUL adapters */
    QVector<MysqlMtaSingleTableAdapter *> adapters;

    /** outer dim -> prow, inner dim -> elen */
    QVector<QVector<MysqlMtaSingleTableAdapter *>> adaptersGrid;

    /** id extras for every table, same hierarchy with tableAdapters */
    QVector<QByteArray> idExtras;

    /** assembly object version adapters are used for */
    qint32 version;

    /** effective length ranges */
    QVector<U2Region> elenRanges;

    /** prow range per table */
    qint32 rowsPerRange;

    //TODO: add read-locks into all methods
    QReadWriteLock tablesSyncLock;

    static const int DEFAULT_ROWS_PER_TABLE = 5000;
    static const int N_READS_TO_FLUSH_TOTAL = 100000;
    static const int N_READS_TO_FLUSH_PER_RANGE = 10000;
};

class MysqlReadTableMigrationData {
public:
    MysqlReadTableMigrationData();
    MysqlReadTableMigrationData(qint64 oldId, MysqlMtaSingleTableAdapter *oldT, int newP);

    qint64 readId;
    MysqlMtaSingleTableAdapter *oldTable;
    int newProw;
};

class MysqlMultiTablePackAlgorithmAdapter : public PackAlgorithmAdapter {
public:
    MysqlMultiTablePackAlgorithmAdapter(MysqlMultiTableAssemblyAdapter *a);
    ~MysqlMultiTablePackAlgorithmAdapter();

    virtual U2DbiIterator<PackAlgorithmData> *selectAllReads(U2OpStatus &os);
    virtual void assignProw(const U2DataId &readId, qint64 prow, U2OpStatus &os);

    void releaseDbResources();
    void migrateAll(U2OpStatus &os);

private:
    void ensureGridSize(int nRows);
    void migrate(MysqlMtaSingleTableAdapter *newA, const QVector<MysqlReadTableMigrationData> &data, qint64 migratedBefore, qint64 totalMigrationCount, U2OpStatus &os);

    MysqlMultiTableAssemblyAdapter *multiTableAdapter;
    QVector<MysqlSingleTablePackAlgorithmAdapter *> packAdapters;
    QVector<QVector<MysqlSingleTablePackAlgorithmAdapter *>> packAdaptersGrid;
    QHash<MysqlMtaSingleTableAdapter *, QVector<MysqlReadTableMigrationData>> migrations;

    static const int MAX_PERCENT_TO_REINDEX = 20;
};

// Class that multiplexes multiple read iterators into 1
class MysqlMtaReadsIterator : public U2DbiIterator<U2AssemblyRead> {
public:
    MysqlMtaReadsIterator(QVector<U2DbiIterator<U2AssemblyRead> *> &iterators, const QVector<QByteArray> &idExtras, bool sortedHint);

    virtual ~MysqlMtaReadsIterator();

    virtual bool hasNext();

    virtual U2AssemblyRead next();

    virtual U2AssemblyRead peek();

private:
    QVector<U2DbiIterator<U2AssemblyRead> *> iterators;
    int currentRange;
    QVector<QByteArray> idExtras;
    bool sortedHint;
};

// Class that multiplexes multiple read packed data iterators into 1 and supports ordering
class MysqlMTAPackAlgorithmDataIterator : public U2DbiIterator<PackAlgorithmData> {
public:
    MysqlMTAPackAlgorithmDataIterator(QVector<U2DbiIterator<PackAlgorithmData> *> &iterators, const QVector<QByteArray> &idExtras);

    virtual ~MysqlMTAPackAlgorithmDataIterator();

    virtual bool hasNext();

    virtual PackAlgorithmData next();

    virtual PackAlgorithmData peek();

private:
    void fetchNextData();

    QVector<U2DbiIterator<PackAlgorithmData> *> iterators;
    PackAlgorithmData nextData;
    QVector<QByteArray> idExtras;
};

}    // namespace U2

#endif    // _U2_MYSQL_ASSEMBLY_MULTI_TABLE_DBI_H_
